Consider as an example this regression test: jdk/test/java/awt/Mixing/AWT_Mixing/JButtonInGlassPaneOverlapping.java
It has a superclass in the same directory and I'm sorry to say even two superclasses (GlassPaneOverlappingTestBase, OverlappingTestBase).
Only the latter one has code with internal calls but it is not a test per se and has no place for annotation. So [at]modules goes to the trivial JButtonInGlassPaneOverlapping.java.
Unfortunately, the test fails at the runtime ("Class OverlappingTestBase can not access a member of class sun.awt.X11.XBaseWindow etc.")

Tested with jtreg-jigsaw built on May 18, 2015 and jake build from May 19.